Gearing: There is not just one answer. Everyone has an opinion. But gearing MUST be coordinated with tire size. The stock, stiff, suspension will accommodate 215/75R15's without modifications. Larger tires mean suspension modifications (lift/springs/shackles) and wider wheels will likely be required, and your speedo will read low. Lower transfer-case gears do not affect speedo accuracy, but low T-case gearsets often require reinforcement of the mounting arms, a common problem with too many solutions. Increasing Ring & Pinion (reduction) gearing (F&R) according to the increase in tire diameter is one way to keep the speedo close and minimize stresses on the rest of the drivetrain. But there are at least 5 popular transfer-case gearsets, and everyone seems to have a favorite. Suzuki Sidekick R&P (front) gears will fit the Samurai, and there are a few (3-4+) higher ratios available. How you intend to use your Zuk will have much influence on your choices. Highway gearing can be the most difficult/critical to get right, as the engine has barely enough power. Assuming Suzuki engineers got it pretty close to right, you can plan to increase the overall highway reduction according to the increase in tire size, percent for percent, to keep your 5th gear usable. Early Zuks (pre-'88.5) had a higher (lower numerically) 5th gear which was lowered later by 8-9%, providing better pulling ability for a few hundred additional RPM. Except for that one 5th gear change, all Samurai transmissions have the same gearing.
Vibration: There are SIX U-joints. After replacing them ALL, I finally tracked down my vibration to a bad intermediate shaft, between the transmission and the transfer case. It was both out-of-balance AND had a bad U-joint. Transfer-case and motor mounts can look good but be bad/broken -- check carefully.
Edit: With 30" tires, 4:1 transfer-case gears may be all you need. The additional high-range reduction will make 5th gear work again on the highway, and you'll get a great low range for off-road. Early Zuks had a higher 5th gear, so you could consider the 4.9 gearset with more (16 or 18%) high-range reduction. Later Zuks had a lower 5th OD gear for more pulling power, so the 4.16:1 T-case with the 12% additional high-range reduction could work well.